That's probably the shader cache being generated. Whenever Dolphin encounters a new shader that it hasn't come across yet, it needs to be generated right away, which leads to a slight stutter in the game. If you replay that part of the game on the same Dolphin build, the stutter will be gone.
As of right now, there is no available fix, but solutions are being worked on by the developers.
You could also try the Ishiiruka unofficial build, as that has async shader compilation, meaning it has a black area where the shader goes while the shader is being compiled. However, that branch is unofficial, so you may run into issues that aren't in the master branch and can only get support in that thread.